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| Status |
Public on Sep 09, 2020 |
| Title |
The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Circular RNAs (circRNAs) represent an abundant and conserved entity of non-coding RNAs, however the principles of biogenesis are currently not fully understood. To elucidate features important for circRNA production, we performed global analyses of RNA-binding proteins associating with the flanking introns of circRNAs, and we identified two factors, SFPQ and NONO, to be highly enriched with circRNAs. We observe a subclass of circRNAs, coined DALI circRNAs, with distal inverted Alu elements and long introns to be highly deregulated upon SFPQ knockdown. Moreover, SFPQ depletion leads to increased intron retention with concomitant induction of cryptic splicing prevalent for long introns causing in some cases premature transcription termination and polyadenylation. Aberrant splicing in the upstream and downstream regions of circRNA producing exons are critical for shaping the circRNAome, and specifically, we identify a conserved impact of missplicing in the immediate upstream region to drive circRNA biogenesis. Collectively, our data show that SFPQ plays an important role in maintaining intron integrity by ensuring accurate splicing of long introns, and disclose novel features governing Alu-independent circRNA production.
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| Overall design |
Total RNA sequencing and quantSeq on RNA from HepG2 and HEK293T subjected to SFPQ and NONO depletion
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| Contributor(s) |
Hansen TB, Stagsted LV |
| Citation(s) |
33476259 |
| Submission date |
Sep 08, 2020 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Thomas B Hansen |
| E-mail(s) |
tbh@mbg.au.dk
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| Phone |
20733619
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| Organization name |
MBG, Aarhus University
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| Street address |
C.F. Moellers Alle 3, build 1130
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| City |
Aarhus C |
| State/province |
State... |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL23227 |
BGISEQ-500 (Homo sapiens) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA662248 |
| SRA |
SRP281189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157622_HEK293T_ciri2.txt.gz |
125.5 Kb |
(ftp)(http) |
TXT |
| GSE157622_HEK293T_featureCounts.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE157622_HEK293T_find_circ.txt.gz |
177.7 Kb |
(ftp)(http) |
TXT |
| GSE157622_HEK293T_peakcall_minus_featureCounts.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE157622_HEK293T_peakcall_plus_featureCounts.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE157622_HepG2_ciri2.txt.gz |
207.3 Kb |
(ftp)(http) |
TXT |
| GSE157622_HepG2_find_circ.txt.gz |
228.4 Kb |
(ftp)(http) |
TXT |
| GSE157622_hepG2_featureCounts.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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